CCopybara-ServiceAdd the glycan modeling paper in the list of community tools

Community Tools

JAAG: a JSON input file Assembler for AlphaFold 3 (with Glycan Integration)

JAAG is a lightweight, web-based GUI tool that helps generate AlphaFold 3 input JSON files with integrated glycan support. It automates the creation of correct glycan syntax (including bondedAtomPairs + CCD), reducing manual errors when preparing glycoprotein or glycan–protein complexes.

Web app: https://biofgreat.org/JAAG
Source code: https://github.com/chinchc/JAAG
Paper: https://doi.org/10.1093/glycob/cwaf083

Note: JAAG is compatible with standalone AlphaFold 3, but not with the AlphaFold 3 server.

Modeling glycans with AlphaFold 3: capabilities, caveats, and limitations

Paper on modeling glycans (and other ligands) with AF3 that modeled and assessed major glycan classes and provides:

Step-by-step tutorial for building ligand inputs (applicable beyond glycans)
Ready-to-run scripts for each glycan class
Comprehensive CCD table for all SNFG monosaccharides
Discussion of caveats and limitations of AF3
Full AF3 inputs/outputs archived on ModelArchive for reproducibility

Useful resource if your AF3 ligand models appear stereochemically off.

Paper: https://doi.org/10.1093/glycob/cwaf048
ModelArchive: https://doi.org/10.5452/ma-af3glycan